We are investigating the details of high resolution structures of DNA quadruplexes and DNA-ligand complexes as determined by Nuclear Magnetic Resonance Spectroscopy (NMR). Using MidasPlus, and other programs we have arrived at three-dimensional structures for many of these species. Extensive molecular dynamics (MD) is performed using AMBER and the Particle Mesh Ewald (PME) summation method for dealing with long-range electrostatic interactions. The "movie" program, "DISPLAY," is used extensively to view these simulations, while others, such as NOEshow are used to discern regions where the molecules best fit the NMR data. The structure of the sequence [d(G3T4G3)]2 is now being studied using DOCK to identify various ligands. Our work on the DNA-peptide conjugate also continues, as we explore the binding mode and sequence specificity using many of the same techniques.